Staying near Shinjuku Station is one of the easiest ways to build a Tokyo trip around trains. You get access to the Yamanote line loop plus multiple Tokyo Metro and Toei lines, which makes day trips and late-night returns simpler than many other areas.
The trade-off is that Shinjuku is busy, and different blocks feel very different at night. If you plan to use trains frequently (or you like dining and bars that run late), choosing the right neighbourhood side matters.
Below are the most useful places to base yourself for easy transfers and late-night convenience, and how to match your hotel pick to how you actually travel.